#!/usr/bin/perl

use warnings;
use strict;

my %snps;
my %iupac;
$iupac{'A'}{'R'} = 'G';
$iupac{'A'}{'W'} = 'T';
$iupac{'A'}{'M'} = 'C';
$iupac{'A'}{'Y'} = 'C|T';
$iupac{'A'}{'K'} = 'G|T';
$iupac{'A'}{'S'} = 'G|C';
$iupac{'G'}{'R'} = 'A';
$iupac{'G'}{'S'} = 'C';
$iupac{'G'}{'K'} = 'T';
$iupac{'G'}{'Y'} = 'C|T';
$iupac{'G'}{'W'} = 'A|T';
$iupac{'G'}{'M'} = 'A|C';
$iupac{'C'}{'Y'} = 'T';
$iupac{'C'}{'S'} = 'G';
$iupac{'C'}{'M'} = 'A';
$iupac{'C'}{'R'} = 'A|G';
$iupac{'C'}{'W'} = 'A|T';
$iupac{'C'}{'K'} = 'G|T';
$iupac{'T'}{'Y'} = 'C';
$iupac{'T'}{'W'} = 'A';
$iupac{'T'}{'K'} = 'G';
$iupac{'T'}{'R'} = 'A|G';
$iupac{'T'}{'S'} = 'G|C';
$iupac{'T'}{'M'} = 'A|C';

my $snpFilteredPileupFile = $ARGV[0];

open (SNP, "<$snpFilteredPileupFile");

while (<SNP>) {
	chomp;
	my ($chr, $pos, $ref, $cons, $consQual, $depth, $baseString) = (split /\t/, $_)[0,1,2,3,4,7,8];
	$ref = uc $ref;
	my $snp = ($cons =~ m/[AGCT]/) ? $cons : $iupac{$ref}{$cons};
	$snps{$chr}{$pos}{'ref'} = $ref;
	$snps{$chr}{$pos}{'snp'} = $snp;
	$snps{$chr}{$pos}{'qual'} = $consQual;
	my $snpCount;
	if ($snps{$chr}{$pos}{'snp'} eq 'A') {
		$snpCount = $baseString =~ tr/Aa/Aa/;
	} elsif ($snps{$chr}{$pos}{'snp'} eq 'C') {
		$snpCount = $baseString =~ tr/Cc/Cc/;
	} elsif ($snps{$chr}{$pos}{'snp'} eq 'G') {
		$snpCount = $baseString =~ tr/Gg/Gg/;
	} elsif ($snps{$chr}{$pos}{'snp'} eq 'T') {
		$snpCount = $baseString =~ tr/Tt/Tt/;
	} elsif ($snps{$chr}{$pos}{'snp'} eq 'A|C') {
		$snpCount = $baseString =~ tr/AaCc/AaCc/;
	} elsif ($snps{$chr}{$pos}{'snp'} eq 'A|G') {
		$snpCount = $baseString =~ tr/AaGg/AaGg/;
	} elsif ($snps{$chr}{$pos}{'snp'} eq 'A|T') {
		$snpCount = $baseString =~ tr/AaTt/AaTt/;
	} elsif ($snps{$chr}{$pos}{'snp'} eq 'G|C') {
		$snpCount = $baseString =~ tr/GgCc/GgCc/;
	} elsif ($snps{$chr}{$pos}{'snp'} eq 'G|T') {
		$snpCount = $baseString =~ tr/GgTt/GgTt/;
	} elsif ($snps{$chr}{$pos}{'snp'} eq 'C|T') {
		$snpCount = $baseString =~ tr/CcTt/CcTt/;
	}
	$snps{$chr}{$pos}{'depth'} = $depth;
	$snps{$chr}{$pos}{'freq'} = $snpCount . '/' . $depth;
	$snps{$chr}{$pos}{'pct'} = sprintf '%.2f', ($snpCount/$depth);
}

close SNP;

foreach my $chr (sort keys %snps) {
	foreach my $pos (sort {$a <=> $b} keys %{ $snps{$chr} }) {
		print "$chr\t$pos\t${snps{$chr}{$pos}{'ref'}} > ${snps{$chr}{$pos}{'snp'}}\t${snps{$chr}{$pos}{'qual'}}\t${snps{$chr}{$pos}{'depth'}}\t${snps{$chr}{$pos}{'freq'}}\t${snps{$chr}{$pos}{'pct'}}\n";
	}
}